Download the program ('Download ZIP button') and unzip it. To run the program only the file depth-cover.jar is needed. Execute depth-cover with: java -XmxMAX_MEMORY_ALLOCATION -jar depth-cover.jar -bam BAM_FILE [OPTIONS] Options are detailed in the help. To see the help type: java -jar depth-cover.jar 

depth-cover consumes files in BAM format. By default it calculates the coverage of the genome used for the alignemnt. Optionally, it accepts a BED file to calculate the coverage in specific interval(s) [-bed option]. To calculate the coverage without taking into account the Ns in the reference a FASTA file can be provided [-fasta option]. depth-cover produces 4 output files: *.summary.csv - number of reads and the mean coverage per genome and chromosomes / intervals. *.coverage.csv - coverage per genome / intervals. *.breakdown.csv - coverage per chromosome / interval. *.details.csv - coverage per locus (optional). 

depth-cover is several orders of magnitude faster than other tools. Execution time and memory consumption depend on the size of the BAM file. In a modern desktop computer, it can process 15-30 million reads per minute. Recommended memory allocation is 15% - 50% of the size of the BAM file - i.e.: if your BAM is 10Gb, execute like: java -Xmx2g -XX:+UseParallelGC -jar depth-cover.jar ARGUMENTS The JVM option -XX:+UseParallelGC is not mandatory, but usually it is a good idea (particularly, if memory is a scarce resource). If the BAM file is indexed and bigger than 4 Gb, and there is enough memory, depth-cover will read the chromosomes in parallel, performing up to 50% faster. The parallel reader makes intensive use of CPU and RAM. If you use a shared computer, you might want to disable it with the --ignore-index option. 

If the parallel reader is enabled (see above) and one chromosome has zero reads, depth-cover will hang. The --ignore-index flag solves this issue. Processing intervals in a not indexed BAM file takes as much time as it would take for the whole genome. It is highly recommended to use indexed BAM files for interval processing. depth-cover uses samtools-1.108. Any bug in this library might affect depth-cover as well. 

Not all the resources for unit tests are included. This means that if you try to run 'mvn install' it will fail. The missing resources are available under request.